The capabilities of the recent MAL (Milling-Assisted Loading) method were analyzed for the geometric confinement of amino acids within mesoporous silica matrices. The present study has shown a high filling degree (45 wt%) of L-tryptophan into unmodified MCM-41 pores. It was shown that the low-frequency Raman spectroscopy is a suited technique to determine that molecular materials are actually confined into silica-based ordered mesoporous materials from the analysis of lattice mode region, and to probe the molecular conformation of confined materials and their interaction with the pore surface from the analysis of internal vibrations.